TransPi

TransPi assembles de novo transcriptomes from RNA-Seq data to generate high-quality, reduced-redundancy consensus transcriptome assemblies for downstream analyses in non-model organisms.

Key Features:

• Workflow engine: Implemented on the Nextflow workflow manager for automated execution of the computational pipeline.
• Multi-assembler strategy: Employs multiple assemblers and parameter sets to produce a consensus assembly and minimize redundancy.
• Automated RNA-Seq processing: Provides an automated pipeline for RNA-Seq data processing and assembly generation.
• Quality assessment tools: Integrates BUSCO for completeness evaluation, TransDecoder for open reading frame (ORF) prediction, and Trinotate for gene ontology annotation.
• Performance metrics: Produces assemblies with higher BUSCO completeness percentages and reduced duplication rates relative to single-assembler approaches.
• Validation on diverse taxa: Evaluated on 49 non-model organisms spanning multiple phyla.

Scientific Applications:

• Differential gene expression: Provides reference transcriptomes for RNA-Seq–based differential expression analyses.
• DNA enrichment bait design: Supplies assembled transcript sequences suitable for designing DNA enrichment baits.
• Phylogenetics: Enables phylogenetic studies using transcriptomic data from non-model species.
• Reference transcriptome generation: Produces reduced-redundancy transcriptomes to explore genetic diversity and evolutionary relationships in species lacking genomes.

Methodology:

Built on Nextflow, the pipeline applies a multi-assembler approach with multiple parameter sets to create a consensus assembly, evaluates completeness with BUSCO, predicts ORFs with TransDecoder, and performs annotation with Trinotate using RNA-Seq input.